Digital switch mode power supply (SMPS) power conversion applications are becoming increasingly more sophisticated in having multiple sub-circuits that utilize multiple pulse width modulation (PWM) signals that may operate at different frequencies and/or phase shifts. When externally synchronizing multiple phase shifted PWM signals, or groups of PWM signal channels with differing frequencies, conventional methods of generating the multiple phase shifted PWM signals cannot maintain proper phase relationships between the PWM signals following a synchronization event. Most present technology PWM controllers are implemented with analog circuitry which does not support advanced PWM protocols, and most digital PWM controllers were designed for simple motor control which also does not support advanced PWM protocols.